The traditional classification of nucleic acid polymerases as either DNA or RNA polymerases is based, in large part, on their fundamental preference for the incorporation of either deoxyribonucleotides or ribonucleotides during chain elongation. The refined structure determination of Moloney murine leukemia virus reverse transcriptase, a strict DNA polymerase, recently allowed the prediction that a single amino acid residue at the active site might be responsible for the discrimination against the 2'OH group of an incoming ribonucleotide. Mutation of this residue resulted in a variant enzyme now capable of acting as an RNA polymerase. In marked contrast to the wild-type enzyme, the K.sub.m of the mutant enzyme for ribonucleotides was comparable to that for deoxyribonucleotides. The results are consistent with proposals of a common evolutionary origin for both classes of enzymes, and support models of a common mechanism of nucleic acid synthesis underlying catalysis by all such polymerases.
A key characteristic of nucleic acid polymerases is their traditional classification as either DNA or RNA polymerases, which is determined by a given enzyme's ability to selectively use either deoxyribonucleotides (dNTPs) or ribonucleotides (rNTPs) as substrates for incorporation into a growing chain (1, 2). This classification, however, may not be as fundamental as originally thought (3-5). Crystallographic studies have demonstrated that DNA and RNA polymerases have remarkable structural similarities (refs. 6-15, reviewed in ref. 16), even though they lack extensive primary sequence homology. Both have a characteristic protein fold forming a nucleic acid binding cleft, and a trio of carboxylic acid residues thought to participate directly in catalysis through two bound divalent metal ions. Steady-state analyses further support the notion of a common stepwise polymerization mechanism (17, 18). These observations suggest that it might be possible to convert a DNA polymerase into an RNA polymerase by relatively minor alterations in its structure.
Reverse transcriptases (RTs), encoded by all retroviruses, play a defining role in the retroviral life cycle (refs 19 & 20; for reviews see ref. 21). The enzyme is responsible for the synthesis of a double-stranded linear DNA copy of the RNA genome, which is subsequently inserted into the host genome to form the integrated proviral DNA. The reverse transcription reaction is complex, requiring RNA-dependent DNA polymerase activity, DNA-dependent DNA polymerase activity, and an associated RNase activity specific for RNA in RNA:DNA hybrid form (22). Although the enzyme can copy either RNA or DNA templates, RT, like all DNA polymerases, can only use deoxyribonucleotides, and not ribonucleotides as substrates. Studies of the HIV-1 RT have permitted modeling of the position of the incoming nucleotide at the active site (23, 24), with .alpha.-helices C and E, and .beta.-sheet strands 6, and 9-11, setting the major topology of the dNTP binding site. A recently determined crystal structure of a catalytic fragment of Moloney murine leukemia virus (MMLV) RT at 1.8 .ANG. resolution has made it possible to visualize how such selectivity for deoxyribonucleotides might be achieved: the enzyme is proposed to discriminate against ribonucleotides through an unfavorable interaction between the aromatic ring of Phe-155 and the 2'OH of the incoming rNTP (ref. 14; see FIG. 1). Here we report that substitution of this residue by valine, as predicted, does indeed render the enzyme capable of incorporating ribonucleotide substrates into products.